Continuity mistake: At the country club, when Troy is going into the bathroom stall we can see the back and front cover of the 'Guns & Ammo' magazine he is looking at, but when he hears the noise and looks around he is holding a different issue of the 'Guns & Ammo' magazine. (00:51:00)
Revealing mistake: When Francis Fratelli is trying to pick up the gun as the Goonies are escaping from the organ, you can see the rocks shaking each time he drops the gun on the ground.
Other mistake: In the Summer Place scene, after Mama Fratelli sets down four glasses of "colored" water for the boys to drink. The next camera angle shows Mouth wiggling his glass in the air as he retorts, "We're supposed to drink this?", Mama snaps back, "It's wet isn't it? Drink it." If you look closely for 2 seconds you can see Corey Feldman is trying very hard to not smirk at this line, while struggling to stay in-character, as Mikey and Data say their next lines.
Continuity mistake: In the scene where Mikey, Data, Mouth and Chunk enter the restaurant, when Mama Fratelli asks, "What do ya want?" Jake Fratelli is behind them with his hand on their shoulders. When the angle changes Jake Fratelli is at the back of the restaurant walking away. (00:30:20)
Continuity mistake: We see Mouth climb down into the fireplace passage after Brand and Andy. We then see a close-up of Stef's pink high-tops descend, being helped by Mouth (we see his rain slicker), who's already down there with Brand and Andy, who are visible in the background. It cuts to a close-up of Stef, with Data's white Nike high-tops climbing down after her. But the next close-up is of Mouth's feet (black Nikes) just coming down as Brand grabs his ankle and says, "Come on!" Impossible since Mouth was already down there. (00:45:20)
Continuity mistake: Chunk is tied to a chair when Jake and Francis leave him in the room with Sloth. When Chunk introduces himself to Sloth, the rope around Chunk's right shoulder has gone up, off the chair, but then manages to lower itself again, back over the chair in following shots. (01:04:05)
Continuity mistake: At the end, when the Fratellis show up on the beach, Chunk and the others run over to Sloth to protect him and Chunk stands on a large boulder. The ground is rocky and the sand is brownish. When Chunk tells Sloth that he'll live with him, in the overhead close-up Chunk is now shorter than Sloth and the ground is pristine off-white sand. (01:44:10)